
% ----------------------------------------------------------------------
%                   LATEX TEMPLATE FOR PhD THESIS
% ----------------------------------------------------------------------

% based on Harish Bhanderi's PhD/MPhil template, then Uni Cambridge
% http://www-h.eng.cam.ac.uk/help/tpl/textprocessing/ThesisStyle/
% corrected and extended in 2007 by Jakob Suckale, then MPI-CBG PhD programme
% and made available through OpenWetWare.org - the free biology wiki


%: Style file for Latex
% Most style definitions are in the external file PhDthesisPSnPDF.
% In this template package, it can be found in ./Latex/Classes/
% \documentclass[twoside,11pt]{Latex/Classes/PhDthesisPSnPDF}
\documentclass[oneside,12pt]{Latex/Classes/PhDthesisPSnPDF}
\externaldocument{0_frontmatter/glossary}
\externaldocument{2/chapter_2}
\externaldocument{3/chapter_3}
\externaldocument{4/chapter_4}
\externaldocument{5/chapter_5}
\externaldocument{6/chapter_6}
\usepackage[T1]{fontenc}
\usepackage[english]{babel}
\linespread{1.10}
\usepackage[T1]{fontenc}


%: Macro file for Latex
% Macros help you summarise frequently repeated Latex commands.
% Here, they are placed in an external file /Latex/Macros/MacroFile1.tex
% An macro that you may use frequently is the figuremacro (see introduction.tex)
\include{Latex/Macros/MacroFile1}
\makeindex


% ----------------------------------------------------------------------
       
% turn of those nasty overfull and underfull hboxes
\hbadness=10000
\hfuzz=50pt



%: --------------------------------------------------------------
%:                  FRONT MATTER: dedications, abstract,..
% --------------------------------------------------------------

\begin{document}
\setpagewiselinenumbers
\modulolinenumbers[5]
\linenumbers


%\language{english}

% sets line spacing
\renewcommand\baselinestretch{1.2}
\baselineskip=18pt plus1pt


%: ----------------------- generate cover page ------------------------

%\maketitle  % command to print the title page with above variables


%: ----------------------- cover page back side ------------------------
% Your research institution may require reviewer names, etc.
% This cover back side is required by Dresden Med Fac; uncomment if needed.
%: ----------------------- abstract ------------------------

% Your institution may have specific regulations if you need an abstract and where it is to be placed in the document. The default here is just after title.

% \include{0_frontmatter/abstract}

% The original template provides and abstractseparate environment, if your institution requires them to be separate. I think it's easier to print the abstract from the complete thesis by restricting printing to the relevant page.
% \begin{abstractseparate}
%   \input{Abstract/abstract}
% \end{abstractseparate}


%: ----------------------- tie in front matter ------------------------



%: ----------------------- contents ------------------------

\setcounter{secnumdepth}{3} % organisational level that receives a numbers
% levels are: 0 - chapter, 1 - section, 2 - subsection, 3 - subsection


%: ----------------------- list of figures/tables ------------------------





%: --------------------------------------------------------------
%:                  MAIN DOCUMENT SECTION
% --------------------------------------------------------------

% the main text starts here with the introduction, 1st chapter,...
\mainmatter

% \renewcommand{\chaptername}{} % uncomment to print only "1" not "Chapter 1"


%: ----------------------- subdocuments ------------------------

% Parts of the thesis are included below. Rename the files as required.
% But take care that the paths match. You can also change the order of appearance by moving the include commands.

\include{1_introduction/introduction}	% background information
% \include{2/chapter_2}						% aims of the project

% \include{3/subdoc}			
% \include{4/XYZ}	
% \include{5/XYZ}
% \include{6/XYZ}
% \include{7/discussion}               % discussion of results
% \include{8/materials_methods}        % description of lab methods




% --------------------------------------------------------------
%:                  BACK MATTER: appendices, refs,..
% --------------------------------------------------------------

% the back matter: appendix and references close the thesis


%: ----------------------- bibliography ------------------------

% The section below defines how references are listed and formatted
% The default below is 2 columns, small font, complete author names.
% Entries are also linked back to the page number in the text and to external URL if provided in the BibTex file.

% PhDbiblio-url2 = names small caps, title bold & hyperlinked, link to page 
%\begin{multicols}{2} % \begin{multicols}{ # columns}[ header text][ space]
%\begin{tiny} % tiny(5) < scriptsize(7) < footnotesize(8) < small (9)

% \bibliographystyle{Latex/Classes/PhDbiblio-url2} % Title is link if provided
\renewcommand{\bibname}{References} % changes the header; default: Bibliography
% \bibliography{9_backmatter/references} % adjust this to fit your BibTex file

\bibliography{9_backmatter/zotero} % adjust this to fit your BibTex file

%\end{tiny}
%\end{multicols}

% --------------------------------------------------------------
% Various bibliography styles exit. Replace above style as desired.

% in-text refs: (1) (1; 2)
% ref list: alphabetical; author(s) in small caps; initials last name; page(s)
%\bibliographystyle{Latex/Classes/PhDbiblio-case} % title forced lower case
%\bibliographystyle{Latex/Classes/PhDbiblio-bold} % title as in bibtex but bold
%\bibliographystyle{Latex/Classes/PhDbiblio-url} % bold + www link if provided


\bibliographystyle{Latex/Classes/jmb} % calls style file jmb.bst
% in-text refs: author (year) without brackets
% ref list: alphabetical; author(s) in normal font; last name, initials; page(s)
%\bibliographystyle{plainnat} % calls style file plainnat.bst
% in-text refs: author (year) without brackets
% (this works with package natbib)


\printindex





\end{document}
